Understanding MakeDOCK, which automates sphere and grid generation

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What is MakeDOCK?

  • MakeDOCK automates the process of sphere and grid generation for a target.

Input files to MakeDOCK

  • Create a new directory containing the following input files to MakeDOCK:
  1. rec.pdb: Prepared receptor file
  2. xtal-lig.pdb: Ligand specification file

These are required to specify the target for docking. For help preparing these files, see #Receptor Preparation and #Ligand Preparation below.

How to use MakeDOCK

In the directory containing rec.pdb and xtal-lig.pdb.

setenv DOCK_BASE 

Receptor Preparation

To prepare a typical pdb structure for use as the receptor in MakeDOCK, do the following:

  1. Remove solvent (i.e. crystallographic waters)
  2. Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding)
  3. Remove the ligand itself
  4. Delete all hydrogens
  5. Save as rec_original.pdb
  6. Run 'paranoia.csh' to clean up the rec_original.pdb file into a rec.pdb file

Ligand Preparation

To prepare the ligand specification, reload the original pdb structure and perform the following steps:

  1. Delete everything BUT the ligand atoms
  2. Save as xtal-lig.pdb